@teselagen/ove 0.7.27 → 0.7.28

package/cutsiteTool.js

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+import { Icon, Button, KeyCombo } from "@blueprintjs/core";
+import CutsiteFilter from "../CutsiteFilter";
+import React from "react";
+import ToolbarItem from "./ToolbarItem";
+import { connectToEditor } from "../withEditorProps";
+import { userDefinedHandlersAndOpts } from "../Editor/userDefinedHandlersAndOpts";
+import { pick } from "lodash-es";
+
+export default connectToEditor(
+  ({ readOnly, annotationVisibility = {}, toolBar = {} }) => {
+    return {
+      readOnly,
+      toggled: annotationVisibility.cutsites,
+      isOpen: toolBar.openItem === "cutsiteTool"
+    };
+  }
+)(({ toolbarItemProps, toggled, isOpen, annotationVisibilityToggle }) => {
+  return (
+    <ToolbarItem
+      {...{
+        Icon: <Icon data-test="cutsiteHideShowTool" icon="cut" />,
+        onIconClick: function () {
+          annotationVisibilityToggle("cutsites");
+        },
+        toggled,
+        tooltip: "Show cut sites",
+        tooltipToggled: "Hide cut sites",
+        Dropdown: CutsiteToolDropDown,
+        dropdowntooltip: (!isOpen ? "Show" : "Hide") + " Cut Site Options",
+        ...toolbarItemProps
+      }}
+    />
+  );
+});
+// import show_cut_sites_img from "./veToolbarIcons/show_cut_sites.png";
+
+// function CutsiteToolIcon({ annotationVisibilityToggle }) {
+//   return (
+//     <div
+//       onClick={function() {
+//         annotationVisibilityToggle("cutsites");
+//       }}
+//     >
+//       <img src={show_cut_sites_img} alt="Show cut sites" />
+//     </div>
+//   );
+// }
+
+function CutsiteToolDropDown({
+  editorName,
+  toggleDropdown,
+  annotationVisibilityShow,
+  withDigestTool,
+  createNewDigest,
+
+  ...rest
+}) {
+  return (
+    <div className="veToolbarCutsiteFilterHolder">
+      <h6>
+        Filter Cut Sites{" "}
+        <span style={{ fontSize: 12, color: "grey" }}>
+          (Search by name or # of cuts)
+        </span>
+      </h6>
+      <CutsiteFilter
+        {...pick(rest, userDefinedHandlersAndOpts)}
+        editorName={editorName}
+        onChangeHook={function () {
+          annotationVisibilityShow("cutsites");
+        }}
+        closeDropDown={() => toggleDropdown({ forceClose: true })}
+      />
+      {withDigestTool && (
+        <Button
+          onClick={() => {
+            createNewDigest();
+            toggleDropdown();
+          }}
+        >
+          <span style={{ display: "flex" }}>
+            Virtual Digest &nbsp; <KeyCombo minimal combo="mod+shift+d" />
+          </span>
+        </Button>
+      )}
+    </div>
+  );
+}

package/cutsitesByRangeSelector.js

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+// import cutsitesSelector from './cutsitesSelector';
+// export default function (state) {
+// 	var {cutsites} = cutsitesSelector(state)
+
+// }

package/cutsitesSelector.js

@@ -0,0 +1,61 @@
+import shortid from "shortid";
+import circularSelector from "./circularSelector";
+import sequenceSelector from "./sequenceSelector";
+import restrictionEnzymesSelector from "./restrictionEnzymesSelector";
+import cutsiteLabelColorSelector from "./cutsiteLabelColorSelector";
+import { createSelector } from "reselect";
+
+import { flatMap as flatmap, map } from "lodash-es";
+import { getCutsitesFromSequence } from "@teselagen/sequence-utils";
+import { getLowerCaseObj } from "../utils/arrayUtils";
+
+function cutsitesSelector(sequence, circular, enzymeList, cutsiteLabelColors) {
+  //get the cutsites grouped by enzyme
+  const cutsitesByName = getLowerCaseObj(
+    getCutsitesFromSequence(sequence, circular, map(enzymeList))
+  );
+  //tag each cutsite with a unique id
+  const cutsitesById = {};
+  Object.keys(cutsitesByName).forEach(function (enzymeName) {
+    const cutsitesForEnzyme = cutsitesByName[enzymeName];
+    cutsitesForEnzyme.forEach(function (cutsite) {
+      const numberOfCuts = cutsitesByName[enzymeName].length;
+      const uniqueId = shortid();
+      cutsite.id = uniqueId;
+      cutsite.numberOfCuts = numberOfCuts;
+      cutsite.annotationType = "cutsite";
+      cutsitesById[uniqueId] = cutsite;
+      const mergedCutsiteColors = Object.assign(
+        { single: "salmon", double: "lightblue", multi: "lightgrey" },
+        cutsiteLabelColors
+      );
+      if (numberOfCuts === 1) {
+        cutsite.labelColor = mergedCutsiteColors.single;
+        cutsite.labelClassname = "singleCutter";
+      } else if (numberOfCuts === 2) {
+        cutsite.labelColor = mergedCutsiteColors.double;
+        cutsite.labelClassname = "doubleCutter";
+      } else {
+        cutsite.labelColor = mergedCutsiteColors.multi;
+        cutsite.labelClassname = "multiCutter";
+      }
+    });
+  });
+  // create an array of the cutsites
+  const cutsitesArray = flatmap(cutsitesByName, function (cutsitesForEnzyme) {
+    return cutsitesForEnzyme;
+  });
+  return {
+    cutsitesByName,
+    cutsitesById,
+    cutsitesArray
+  };
+}
+
+export default createSelector(
+  sequenceSelector,
+  circularSelector,
+  restrictionEnzymesSelector,
+  cutsiteLabelColorSelector,
+  cutsitesSelector
+);

package/darkmode.css

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+.bp3-dark .veAxisLine {
+  stroke: #f5f8fa !important;
+}
+.bp3-dark .veAxisTick,
+.bp3-dark .veCutsite {
+  fill: #f5f8fa;
+}
+
+.bp3-dark .veEditor:not(.tg-simple-dna-view) {
+  background: #293742 !important;
+}
+
+.veLabelLine {
+  stroke: black;
+  background: black;
+}
+.bp3-dark .veCaret,
+.bp3-dark .veLabelLine {
+  stroke: white;
+  background: white;
+}
+.bp3-dark .veLabelLine {
+  stroke: #f5f8fa !important;
+  background: #f5f8fa !important;
+}
+
+.bp3-dark .veEditor .veRowViewCaret {
+  background: #f5f8fa !important;
+}
+
+.bp3-dark .veEditor text {
+  fill: #f5f8fa;
+}
+
+.bp3-dark .veRowViewPartsContainer text,
+.bp3-dark .veLabelText.black {
+  fill: #f5f8fa !important;
+}
+
+.bp3-dark .tag-selection.selected {
+  border-color: #f5f8fa !important;
+}
+
+.bp3-dark .veLinearView text {
+  fill: #f5f8fa !important;
+}
+.bp3-dark .veCircularViewAxisNumber rect {
+  fill: #f5f8fa !important;
+}
+
+.bp3-dark .menu-bar {
+  background: none !important;
+}
+
+.alignmentViewTrackContainer {
+  background: white;
+}
+.bp3-dark .alignmentViewTrackContainer {
+  background: #293742;
+}
+.bp3-dark .alignmentViewTrackContainer text {
+  fill: #f5f8fa !important;
+}
+
+/* .bp3-dark .veRowViewAxis text {
+  stroke: #f5f8fa !important;
+} */
+
+.bp3-dark .translationLayer text {
+  fill: black !important;
+}
+
+.bp3-dark .step-group.active .step-text {
+  color: #2b95d6 !important;
+}
+
+.bp3-dark .step-group.active .step-mark {
+  background-color: #2b95d6 !important;
+  border-color: #2b95d6 !important;
+}
+
+.bp3-dark .tool-select-item:hover {
+  background: #0e5a8a !important;
+}
+
+.bp3-dark .veWhiteBackground {
+  background: #293742;
+}
+
+.bp3-dark .vePart path:first-of-type {
+  stroke-width: 1;
+  stroke: #df7ff1 !important;
+}
+
+.bp3-dark .vePart .veLabelText,
+.bp3-dark .veLabelText.vePart {
+  fill: #ac68cc !important;
+}

package/defaultConfig.js

@@ -0,0 +1,150 @@
+//only things specific to this menu should be included here
+//things that are shared between multiple menus, or that are command specific should be
+//defined in the commands/index.js file
+
+import viewSubmenu from "./viewSubmenu";
+export const copyOptionsMenu = {
+  text: "Copy Options",
+  showInSearchMenu: true,
+  submenu: [
+    { cmd: "toggleCopyFeatures", shouldDismissPopover: false },
+    { cmd: "toggleCopyPartialFeatures", shouldDismissPopover: false },
+    { cmd: "toggleCopyParts", shouldDismissPopover: false },
+    { cmd: "toggleCopyPartialParts", shouldDismissPopover: false }
+  ]
+};
+export const createNewAnnotationMenu = {
+  text: "Create",
+  cmd: "createMenuHolder",
+  showInSearchMenu: true
+};
+export default [
+  {
+    text: "File",
+    "data-test": "file",
+    submenu: [
+      {
+        cmd: "newSequence",
+        "data-test": "newSequence"
+      },
+      "renameSequence",
+      "saveSequence",
+      "saveSequenceAs",
+      "deleteSequence",
+      "duplicateSequence",
+      "--",
+      { cmd: "toggleReadOnlyMode", shouldDismissPopover: false },
+      "--",
+      "importSequence",
+      {
+        text: "Export Sequence",
+        showInSearchMenu: true,
+        submenu: [
+          { cmd: "exportSequenceAsGenbank" },
+          { cmd: "exportDNASequenceAsFasta" },
+          { cmd: "exportProteinSequenceAsFasta" },
+          { cmd: "exportSequenceAsTeselagenJson" }
+        ]
+      },
+      "--",
+      {
+        text: "Print",
+        cmd: "print"
+        // submenu: [{ cmd: "printCircularView" }, { cmd: "printLinearView" }]
+      },
+      { cmd: "viewRevisionHistory", text: "Revision History" },
+      { cmd: "viewProperties", text: "Properties", icon: "properties" }
+    ]
+  },
+  {
+    text: "Edit",
+    submenu: [
+      createNewAnnotationMenu,
+      "--",
+      "cut",
+      "copy",
+      copyOptionsMenu,
+      "paste",
+      "--",
+      "undo",
+      "redo",
+      "--",
+      "find",
+      "goTo",
+      "--",
+      "select",
+      "selectAll",
+      "selectInverse",
+      {
+        text: "Change Case",
+        cmd: "changeCaseCmd",
+        submenu: [
+          "flipCaseSequence",
+          "upperCaseSequence",
+          "lowerCaseSequence",
+          "upperCaseSelection",
+          "lowerCaseSelection"
+        ]
+      },
+      {
+        text: "Change Circular/Linear",
+        cmd: "changeCircularityCmd",
+        submenu: ["toggleCircular", "toggleLinear"]
+      },
+      // {
+      //   text: "Change Sequence Case For Selection",
+      //   submenu: [
+      //   ]
+      // },
+      "--",
+      "complementSelection",
+      "complementEntireSequence",
+      "reverseComplementSelection",
+      "reverseComplementEntireSequence",
+      "rotateToCaretPosition"
+    ]
+  },
+  {
+    text: "View",
+    submenu: viewSubmenu
+  },
+  {
+    text: "Tools",
+    cmd: "toolsCmd",
+    submenu: [
+      "openFilterCutsites",
+      "restrictionEnzymesManager",
+      "openCreateCustomEnzyme",
+      "simulateDigestion",
+      "simulatePCR",
+      {
+        text: "Remove Duplicates",
+        submenu: [
+          "showRemoveDuplicatesDialogFeatures",
+          "showRemoveDuplicatesDialogParts",
+          "showRemoveDuplicatesDialogPrimers"
+        ]
+      },
+      {
+        text: "Auto Annotate",
+        cmd: "autoAnnotateHolder",
+        submenu: [
+          "autoAnnotateFeatures",
+          "autoAnnotateParts",
+          "autoAnnotatePrimers"
+        ]
+      }
+    ]
+  },
+  // { isMenuSearch: true }
+  {
+    text: "Help",
+    submenu: [
+      { isMenuSearch: true },
+      "--",
+      "about",
+      { cmd: "versionNumber", shouldDismissPopover: false },
+      "hotkeyDialog"
+    ]
+  }
+];

package/deletionLayers.js

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+//./deletionLayers.js
+import { createReducer } from "redux-act";
+import createAction from "./utils/createMetaAction";
+import omit from "lodash/omit";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const deletionLayerClear = createAction("deletionLayerClear");
+export const deletionLayerUpdate = createAction("DELETION_LAYER_UPDATE");
+export const deletionLayerDelete = createAction("DELETION_LAYER_DELETE");
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [deletionLayerClear]: () => {
+      return {};
+    },
+    [deletionLayerUpdate]: (state, payload) => {
+      return {
+        ...state,
+        [payload.id]: {
+          color: "firebrick",
+          id: payload.id,
+          ...payload.range
+        }
+      };
+    },
+    [deletionLayerDelete]: (state, payload) => {
+      return omit(state, payload.id);
+    }
+  },
+  {}
+);

package/description.js

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+import { createReducer } from "redux-act";
+import createAction from "../utils/createMetaAction";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const sequenceDescriptionUpdate = createAction(
+  "sequenceDescriptionUpdate"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createReducer(
+  {
+    [sequenceDescriptionUpdate]: (state, payload) => {
+      return payload;
+    }
+  },
+  ""
+);

package/digestTool.js

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+import createAction from "./utils/createMetaAction";
+import createMergedDefaultStateReducer from "./utils/createMergedDefaultStateReducer";
+
+// ------------------------------------
+// Actions
+// ------------------------------------
+export const updateSelectedFragment = createAction("updateSelectedFragment");
+export const updateComputePartialDigest = createAction(
+  "updateComputePartialDigest"
+);
+
+// ------------------------------------
+// Reducer
+// ------------------------------------
+export default createMergedDefaultStateReducer(
+  {
+    [updateSelectedFragment]: (state, payload) => {
+      return {
+        ...state,
+        selectedFragment: payload
+      };
+    },
+    [updateComputePartialDigest]: (state, payload) => {
+      return {
+        ...state,
+        computePartialDigest: payload
+      };
+    }
+  },
+  {
+    selectedFragment: undefined,
+    computePartialDigest: false
+  }
+);

package/dnaToColor.js

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+import { DNAComplementMap } from "@teselagen/sequence-utils";
+
+const dnaToColor = {
+  a: "lightgreen",
+  c: "#658fff",
+  g: "yellow",
+  t: "#EE6262"
+};
+export default dnaToColor;
+
+export function getDnaColor(char, isReverse) {
+  return (
+    dnaToColor[
+      isReverse ? DNAComplementMap[char.toLowerCase()] : char.toLowerCase()
+    ] || "lightgrey"
+  );
+}

package/downloadTool.js

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+import React from "react";
+import { Icon, Menu } from "@blueprintjs/core";
+import { createCommandMenu } from "@teselagen/ui";
+import getCommands from "../commands";
+
+import { connectToEditor } from "../withEditorProps";
+import ToolbarItem from "./ToolbarItem";
+import withEditorProps from "../withEditorProps";
+
+export default connectToEditor()(({ toolbarItemProps }) => {
+  return (
+    <ToolbarItem
+      {...{
+        tooltip: "Export",
+        Dropdown,
+        noDropdownIcon: true,
+        onIconClick: "toggleDropdown",
+        Icon: <Icon data-test="veDownloadTool" icon="import" />,
+        ...toolbarItemProps
+      }}
+    />
+  );
+});
+
+const Dropdown = withEditorProps(props => {
+  return (
+    <Menu>
+      {createCommandMenu(
+        [
+          "exportSequenceAsGenbank",
+          "exportDNASequenceAsFasta",
+          "exportProteinSequenceAsFasta",
+          "exportSequenceAsTeselagenJson"
+        ],
+        getCommands({ props })
+      )}
+    </Menu>
+  );
+});

package/draggableClassnames.js

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+export default {
+  caret: "veCaret",
+  selectionStart: "veSelectionLayerStart",
+  selectionEnd: "veSelectionLayerEnd"
+};